Simplified Computational Methods for the Analysis of Protein Flexibility

Igor   B.   Kuznetsov

Abstract

Conformational flexibility is an inherent property of the protein structure. Large scale changes in the protein conformation play a key role in a variety of fundamental biological activities and have been implicated in a number of diseases. The time scales of functionally relevant dynamic processes in proteins generally do not allow the researchers to study them by the means of detailed atomic level simulations. Therefore, less computationally demanding methods based on the coarse grained models of protein structure and bioinformatics approaches are particularly important for the flexibility- related studies. This review is focused on two broad categories of protein flexibility - protein disorder and conformational switches. In the case of protein disorder, a flexible protein segment or entire protein is structurally disordered, meaning that it does not have a well-defined folded 3D structure. In the case of conformational switches, the protein backbone of a flexible segment can change or “switch” from one specific folded 3D conformation to another. In this review, the relative strengths and limitations of the existing computational tools, mostly from the bioinformatics domain, used to study and predict protein disorder and conformational switches will be discussed and the main challenges will be highlighted.

Keywords: structural, change, switch, transition, flexibility, motion, movement, plasticity